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Author: Oliver G. Pybus

  • ORCiD: http://orcid.org/0000-0002-8797-2667
  • Most recently observed institution: Department of Zoology, University of Oxford, Oxford OX1 3SZ, United Kingdom; Royal Veterinary College, Hawkshead, United Kingdom

Rankings

  • All-time downloads: 117,562 (rank: 930 )
  • Categories:
    • bioinformatics: 2,474 (rank: 6,297 )
    • epidemiology: 35,621 (rank: 500 )
    • evolutionary biology: 3,738 (rank: 1,011 )
    • genetics: 2,737 (rank: 7,010 (tie) )
    • genomics: 722 (rank: 30,098 (tie) )
    • immunology: 1,123 (rank: 10,439 (tie) )
    • infectious diseases: 61,941 (rank: 817 )
    • microbiology: 8,330 (rank: 1,904 (tie) )
    • molecular biology: 876 (rank: 7,570 (tie) )

Downloads per author, site-wide

Preprints

COVID-19 herd immunity in the Brazilian Amazon

infectious diseases more details view paper
  • Downloaded 28,790 times
  • Download rankings, all-time:
    • Site-wide: 258
    • In infectious diseases: 95
  • Year to date:
    • Site-wide: 614
  • Since beginning of last month:
    • Site-wide: 43,435

Early evaluation of the Wuhan City travel restrictions in response to the 2019 novel coronavirus outbreak

infectious diseases more details view paper
  • Downloaded 14,972 times
  • Download rankings, all-time:
    • Site-wide: 550
    • In infectious diseases: 197
  • Year to date:
    • Site-wide: 5,821
  • Since beginning of last month:
    • Site-wide: 44,258

Viral infection and Transmission in a large well-traced outbreak caused by the Delta SARS-CoV-2 variant

epidemiology more details view paper
  • Downloaded 12,033 times
  • Download rankings, all-time:
    • Site-wide: 750
    • In epidemiology: 111
  • Year to date:
    • Site-wide: 155
  • Since beginning of last month:
    • Site-wide: 258

A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology

microbiology more details view paper
  • Downloaded 8,330 times
  • Download rankings, all-time:
    • Site-wide: 1,211
    • In microbiology: 113
  • Year to date:
    • Site-wide: 1,034
  • Since beginning of last month:
    • Site-wide: 541

A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage

infectious diseases more details view paper
  • Downloaded 6,829 times
  • Download rankings, all-time:
    • Site-wide: 1,535
    • In infectious diseases: 417
  • Year to date:
    • Site-wide: 7,083
  • Since beginning of last month:
    • Site-wide: 77,112

Evolution and epidemic spread of SARS-CoV-2 in Brazil

infectious diseases more details view paper
  • Downloaded 6,027 times
  • Download rankings, all-time:
    • Site-wide: 1,837
    • In infectious diseases: 470
  • Year to date:
    • Site-wide: 20,868
  • Since beginning of last month:
    • Site-wide: 9,287

The effect of human mobility and control measures on the COVID-19 epidemic in China

epidemiology more details view paper
  • Downloaded 5,748 times
  • Download rankings, all-time:
    • Site-wide: 1,951
    • In epidemiology: 230
  • Year to date:
    • Site-wide: 12,872
  • Since beginning of last month:
    • Site-wide: 94,210

Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil

epidemiology more details view paper
  • Downloaded 4,083 times
  • Download rankings, all-time:
    • Site-wide: 3,152
    • In epidemiology: 331
  • Year to date:
    • Site-wide: 525
  • Since beginning of last month:
    • Site-wide: 14,025

Genomic epidemiology of SARS-CoV-2 in Guangdong Province, China

infectious diseases more details view paper
  • Downloaded 3,920 times
  • Download rankings, all-time:
    • Site-wide: 3,346
    • In infectious diseases: 700
  • Year to date:
    • Site-wide: 6,159
  • Since beginning of last month:
    • Site-wide: 43,431

Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic.

epidemiology more details view paper
  • Downloaded 2,507 times
  • Download rankings, all-time:
    • Site-wide: 6,317
    • In epidemiology: 542
  • Year to date:
    • Site-wide: 56,510
  • Since beginning of last month:
    • Site-wide: 5,282

Routes for COVID-19 importation in Brazil

epidemiology more details view paper
  • Downloaded 2,302 times
  • Download rankings, all-time:
    • Site-wide: 7,155
    • In epidemiology: 587
  • Year to date:
    • Site-wide: 67,559
  • Since beginning of last month:
    • Site-wide: 97,750

Identification of a common deletion in the spike protein of SARS-CoV-2

genetics more details view paper
  • Downloaded 1,888 times
  • Download rankings, all-time:
    • Site-wide: 9,583
    • In genetics: 416
  • Year to date:
    • Site-wide: 42,971
  • Since beginning of last month:
    • Site-wide: 41,297

Establishment & lineage dynamics of the SARS-CoV-2 epidemic in the UK

epidemiology more details view paper
  • Downloaded 1,756 times
  • Download rankings, all-time:
    • Site-wide: 10,659
    • In epidemiology: 794
  • Year to date:
    • Site-wide: 7,244
  • Since beginning of last month:
    • Site-wide: 64,223

Multiple introductions of Zika virus into the United States revealed through genomic epidemiology

epidemiology more details view paper
  • Downloaded 1,728 times
  • Download rankings, all-time:
    • Site-wide: 10,922
    • In epidemiology: 806
  • Year to date:
    • Site-wide: 93,180
  • Since beginning of last month:
    • Site-wide: None

Discovery of a persistent Zika virus lineage in Bahia, Brazil

epidemiology more details view paper
  • Downloaded 1,211 times
  • Download rankings, all-time:
    • Site-wide: 18,537
    • In epidemiology: 1,189
  • Year to date:
    • Site-wide: 102,236
  • Since beginning of last month:
    • Site-wide: 24,185

Epidemiological and ecological determinants of Zika virus transmission in an urban setting.

epidemiology more details view paper
  • Downloaded 1,149 times
  • Download rankings, all-time:
    • Site-wide: 20,030
    • In epidemiology: 1,235
  • Year to date:
    • Site-wide: 103,596
  • Since beginning of last month:
    • Site-wide: None

Epidemiology of the Zika virus outbreak in the Cabo Verde Islands, West Africa

epidemiology more details view paper
  • Downloaded 1,110 times
  • Download rankings, all-time:
    • Site-wide: 21,080
    • In epidemiology: 1,279
  • Year to date:
    • Site-wide: 122,634
  • Since beginning of last month:
    • Site-wide: 29,358

Phylogeographic and phylodynamic approaches to epidemiological hypothesis testing

evolutionary biology more details view paper
  • Downloaded 1,073 times
  • Download rankings, all-time:
    • Site-wide: 22,147
    • In evolutionary biology: 885
  • Year to date:
    • Site-wide: 39,028
  • Since beginning of last month:
    • Site-wide: 54,450

Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak

epidemiology more details view paper
  • Downloaded 1,069 times
  • Download rankings, all-time:
    • Site-wide: 22,250
    • In epidemiology: 1,339
  • Year to date:
    • Site-wide: 123,593
  • Since beginning of last month:
    • Site-wide: 111,691

Parallel Evolution in the Emergence of Highly Pathogenic Avian Influenza A Viruses

evolutionary biology more details view paper
  • Downloaded 901 times
  • Download rankings, all-time:
    • Site-wide: 28,516
    • In evolutionary biology: 1,223
  • Year to date:
    • Site-wide: 77,295
  • Since beginning of last month:
    • Site-wide: 106,804

Evolutionary analyses of base-pairing interactions in DNA and RNA secondary structures

molecular biology more details view paper
  • Downloaded 876 times
  • Download rankings, all-time:
    • Site-wide: 29,638
    • In molecular biology: 809
  • Year to date:
    • Site-wide: 58,572
  • Since beginning of last month:
    • Site-wide: 56,717

Optimal Point Process Filtering and Estimation of the Coalescent Process

bioinformatics more details view paper
  • Downloaded 756 times
  • Download rankings, all-time:
    • Site-wide: 36,415
    • In bioinformatics: 3,966
  • Year to date:
    • Site-wide: 92,184
  • Since beginning of last month:
    • Site-wide: None

Optimal Point Process Filtering for Birth-Death Model Estimation

bioinformatics more details view paper
  • Downloaded 611 times
  • Download rankings, all-time:
    • Site-wide: 48,188
    • In bioinformatics: 4,986
  • Year to date:
    • Site-wide: 117,240
  • Since beginning of last month:
    • Site-wide: 25,528

Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador

infectious diseases more details view paper
  • Downloaded 608 times
  • Download rankings, all-time:
    • Site-wide: 48,458
    • In infectious diseases: 2,993
  • Year to date:
    • Site-wide: 6,500
  • Since beginning of last month:
    • Site-wide: 48,592

Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination

immunology more details view paper
  • Downloaded 603 times
  • Download rankings, all-time:
    • Site-wide: 48,991
    • In immunology: 1,482
  • Year to date:
    • Site-wide: 144,439
  • Since beginning of last month:
    • Site-wide: 55,150

Serial Interval Distribution of SARS-CoV-2 Infection in Brazil

infectious diseases more details view paper
  • Downloaded 598 times
  • Download rankings, all-time:
    • Site-wide: 49,464
    • In infectious diseases: 3,033
  • Year to date:
    • Site-wide: 66,594
  • Since beginning of last month:
    • Site-wide: 78,092

The multifurcating skyline plot

bioinformatics more details view paper
  • Downloaded 572 times
  • Download rankings, all-time:
    • Site-wide: 52,385
    • In bioinformatics: 5,331
  • Year to date:
    • Site-wide: 127,731
  • Since beginning of last month:
    • Site-wide: 67,930

Robust Design for Coalescent Model Inference

bioinformatics more details view paper
  • Downloaded 535 times
  • Download rankings, all-time:
    • Site-wide: 56,884
    • In bioinformatics: 5,706
  • Year to date:
    • Site-wide: 140,784
  • Since beginning of last month:
    • Site-wide: 112,927

Human B cell lineages engaged by germinal centers following influenza vaccination are measurably evolving

immunology more details view paper
  • Downloaded 520 times
  • Download rankings, all-time:
    • Site-wide: 58,772
    • In immunology: 1,761
  • Year to date:
    • Site-wide: 8,242
  • Since beginning of last month:
    • Site-wide: 31,609

A computationally tractable birth-death model that combines phylogenetic and epidemiological data

genomics more details view paper
  • Downloaded 492 times
  • Download rankings, all-time:
    • Site-wide: 62,576
    • In genomics: 4,503
  • Year to date:
    • Site-wide: 29,494
  • Since beginning of last month:
    • Site-wide: 63,562

Emergence and persistence of the Chikungunya virus East-Central-South-African genotype in Northeast Brazil

epidemiology more details view paper
  • Downloaded 491 times
  • Download rankings, all-time:
    • Site-wide: 62,700
    • In epidemiology: 2,784
  • Year to date:
    • Site-wide: 115,473
  • Since beginning of last month:
    • Site-wide: None

Jointly inferring the dynamics of population size and sampling intensity from molecular sequences

genetics more details view paper
  • Downloaded 467 times
  • Download rankings, all-time:
    • Site-wide: 66,265
    • In genetics: 2,919
  • Year to date:
    • Site-wide: 103,885
  • Since beginning of last month:
    • Site-wide: 100,113

The evolutionary dynamics of Oropouche Virus (OROV) in South America

evolutionary biology more details view paper
  • Downloaded 465 times
  • Download rankings, all-time:
    • Site-wide: 66,515
    • In evolutionary biology: 3,465
  • Year to date:
    • Site-wide: 89,019
  • Since beginning of last month:
    • Site-wide: None

Modelling the decay of hotspot motifs in broadly neutralizing antibody lineages

evolutionary biology more details view paper
  • Downloaded 460 times
  • Download rankings, all-time:
    • Site-wide: 67,377
    • In evolutionary biology: 3,500
  • Year to date:
    • Site-wide: 150,272
  • Since beginning of last month:
    • Site-wide: None

Are skyline plot-based demographic estimates overly dependent on smoothing prior assumptions?

genetics more details view paper
  • Downloaded 382 times
  • Download rankings, all-time:
    • Site-wide: 80,714
    • In genetics: 3,524
  • Year to date:
    • Site-wide: 53,478
  • Since beginning of last month:
    • Site-wide: 58,220

Identification of site-specific evolutionary trajectories shared across human betacoronaviruses

evolutionary biology more details view paper
  • Downloaded 382 times
  • Download rankings, all-time:
    • Site-wide: 80,790
    • In evolutionary biology: 4,219
  • Year to date:
    • Site-wide: 12,898
  • Since beginning of last month:
    • Site-wide: 49,099

Vaccine nationalism and the dynamics and control of SARS-CoV-2

epidemiology more details view paper
  • Downloaded 373 times
  • Download rankings, all-time:
    • Site-wide: 82,506
    • In epidemiology: 3,506
  • Year to date:
    • Site-wide: 13,321
  • Since beginning of last month:
    • Site-wide: 35,994

High resolution evolutionary analysis of within-host hepatitis C virus infection

evolutionary biology more details view paper
  • Downloaded 352 times
  • Download rankings, all-time:
    • Site-wide: 86,779
    • In evolutionary biology: 4,513
  • Year to date:
    • Site-wide: 152,604
  • Since beginning of last month:
    • Site-wide: 102,748

Oropouche virus cases identified in Ecuador using an optimised rRT-PCR informed by metagenomic sequencing

genomics more details view paper
  • Downloaded 230 times
  • Download rankings, all-time:
    • Site-wide: 115,126
    • In genomics: 6,543
  • Year to date:
    • Site-wide: 144,776
  • Since beginning of last month:
    • Site-wide: 99,636

Kankasha in Kassala: a prospective observational cohort study of the clinical characteristics, epidemiology, genetic origin, and chronic impact of the 2018 epidemic of Chikungunya virus infection in Kassala, Sudan

infectious diseases more details view paper
  • Downloaded 197 times
  • Download rankings, all-time:
    • Site-wide: 123,230
    • In infectious diseases: 4,966
  • Year to date:
    • Site-wide: 74,206
  • Since beginning of last month:
    • Site-wide: 13,648

Global prevalence and phylogeny of hepatitis B virus (HBV) drug and vaccine resistance mutations

evolutionary biology more details view paper
  • Downloaded 105 times
  • Download rankings, all-time:
    • Site-wide: 143,425
    • In evolutionary biology: 6,952
  • Year to date:
    • Site-wide: 105,071
  • Since beginning of last month:
    • Site-wide: 91,622

Global disparities in SARS-CoV-2 genomic surveillance

epidemiology more details view paper
  • Downloaded 61 times
  • Download rankings, all-time:
    • Site-wide: 149,814
    • In epidemiology: 6,167
  • Year to date:
    • Site-wide: 95,795
  • Since beginning of last month:
    • Site-wide: 2,147

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